def test_delete_variant(real_mongo_adapter, het_variant, case_obj):
## GIVEN a database with one variant that is observed twice
db = real_mongo_adapter.db
case_id = case_obj["case_id"]
db.variant.insert_one({
"_id": get_variant_id(het_variant),
"families": [case_id, "2"],
"observations": 2,
})
mongo_variant = db.variant.find_one()
assert mongo_variant["observations"] == 2
## WHEN deleting the variant for one case
delete_variants(
adapter=real_mongo_adapter,
vcf_obj=[het_variant],
case_obj=case_obj,
case_id="2",
)
mongo_variant = db.variant.find_one()
## THEN assert that one case has been removed from 'families'
assert mongo_variant["families"] == [case_id]
## THEN assert that the observation count is decreased
assert mongo_variant["observations"] == 1
def test_delete_variant(real_mongo_adapter, het_variant, case_obj):
## GIVEN a database with one variant that is observed twice
db = real_mongo_adapter.db
case_id = case_obj['case_id']
db.variant.insert_one({
'_id': get_variant_id(het_variant),
'families': [case_id, '2'],
'observations': 2,
})
mongo_variant = db.variant.find_one()
assert mongo_variant['observations'] == 2
## WHEN deleting the variant for one case
delete_variants(
adapter=real_mongo_adapter,
vcf_obj=[het_variant],
case_obj=case_obj,
case_id='2',
)
mongo_variant = db.variant.find_one()
## THEN assert that one case has been removed from 'families'
assert mongo_variant['families'] == [case_id]
## THEN assert that the observation count is decreased
assert mongo_variant['observations'] == 1
def test_delete_non_existing_variant(mongo_adapter, het_variant, case_obj):
"""docstring for test_load_variants"""
## GIVEN a mongo adapter to an empty database
db = mongo_adapter.db
case_id = case_obj["case_id"]
## WHEN deleting the variants
delete_variants(adapter=mongo_adapter,
vcf_obj=[het_variant],
case_obj=case_obj)
# THEN assert nothing happens
mongo_variant = db.variant.find_one()
assert mongo_variant == None
def test_delete_variants(real_mongo_adapter, het_variant, case_obj):
## GIVEN a database with one variant
db = real_mongo_adapter.db
case_id = case_obj["case_id"]
db.variant.insert_one({
"_id": get_variant_id(het_variant),
"families": [case_id],
"observations": 1,
})
mongo_variant = db.variant.find_one()
assert mongo_variant["families"] == [case_id]
## WHEN deleting the variant
delete_variants(adapter=real_mongo_adapter,
vcf_obj=[het_variant],
case_obj=case_obj)
mongo_variant = db.variant.find_one()
## THEN assert that the variant was not found
assert mongo_variant is None
def test_delete_variants(real_mongo_adapter, het_variant, case_obj):
## GIVEN a database with one variant
db = real_mongo_adapter.db
case_id = case_obj['case_id']
db.variant.insert_one({
'_id': get_variant_id(het_variant),
'families': [case_id],
'observations': 1,
})
mongo_variant = db.variant.find_one()
assert mongo_variant['families'] == [case_id]
## WHEN deleting the variant
delete_variants(adapter=real_mongo_adapter,
vcf_obj=[het_variant],
case_obj=case_obj)
mongo_variant = db.variant.find_one()
## THEN assert that the variant was not found
assert mongo_variant == None